MolNFT v1 · #191227 · protein + DNA + RNA
Iscb and wrna bound to target DNA
8CSZ: “Iscb and wrna bound to target DNA”. Electron microscopy, 2 ligands (MG, ZN), 15 pockets (best druggability 0.87). MolNFT v1 #191227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8CSZ
- Type
- protein + DNA + RNA
- Length
- 730 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iscb; RNA (222-mer); DNA target strand; DNA non-target strand
- Ligands
- MG, ZN
- Pockets
- 15 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Iscb | protein | 494 | 30% helix, 24% strand | — |
| C | RNA (222-mer) | rna | 184 | — | — |
| B | DNA target strand | dna | 33 | — | — |
| E | DNA non-target strand | dna | 19 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.87 | 0.89 | 94 | empty |
| 2 | 1041 | 0.79 | 0.82 | 77 | empty |
| 3 | 1133 | 0.75 | 0.78 | 90 | empty |
| 4 | 910 | 0.71 | 0.77 | 37 | empty |
| 5 | 144 | 0.59 | 0.84 | 16 | empty |
Interfaces
5 interfaces between chains.
- D–C · 6806 Ų buried · 156 hydrogen bonds · protein-nucleic
- D–B · 1861 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–E · 1042 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–B · 780 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- B–E · 681 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Compared structures
- 8CSZ · IscB and wRNA bound to Target DNA · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 8CSZ · PDBe 8CSZ
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